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Parameter: derive from file

Read a one-value dataset with param_value_from_file, including count recipes that feed typed parameters.

draft patterntarget/galaxy
Revised
2026-05-03
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3
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  • IWC exemplar anchors

    4 abstract workflow anchors declared.

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Parameter: derive from file

Tool

Use param_value_from_file when an upstream dataset contains exactly one scalar value that must become a connected Galaxy runtime parameter.

The corpus-backed shape is:

dataset -> param_value_from_file -> downstream tool parameter

param_type selects the typed output port: integer_param, float_param, text_param, or boolean_param. In the observed scalar-read examples, remove_newlines: true is the normal setting.

When to reach for it

Use this when a workflow computes or receives a small file containing one value, and a downstream tool needs that value as a typed parameter rather than as a dataset input.

Good fits include computed genome sizes, coverage estimates, minimum counts, repeat counts, line counts, file-derived text, and boolean shims.

Do not use this for ordinary tabular transformations whose output remains a dataset; use tabular patterns such as tabular-compute-new-column.

Do not use this for dynamic expression strings built directly from parameters; use compose-runtime-text-parameter.

Do not center non-empty gating here. If the user story is “skip downstream work when empty,” use conditional-gate-on-nonempty-result.

Operation Boundary

This pattern covers file-to-parameter bridging:

  • input fact: a dataset contains one scalar value, or an upstream count recipe produces one scalar value;
  • output action: expose that scalar as a Galaxy typed runtime parameter port;
  • bridge mechanism: param_value_from_file.

It covers file-to-integer, file-to-float, file-to-text, file-to-boolean, count-to-integer, and collection-size-to-boolean when explaining the bridge.

It does not cover enum mapping, runtime text composition, branch topology after a boolean exists, general column computation, or collection cleanup.

Parameters

  • input1: connected scalar dataset.
  • param_type: set to integer, float, text, or boolean; downstream steps must connect the matching typed output port.
  • remove_newlines: set true for one-value files unless the downstream text parameter explicitly needs line breaks.

Changing param_type changes which output port is meaningful. A generated workflow must connect integer_param to integer inputs, float_param to float inputs, and so on.

Count, Then Parameterize

Use wc_gnu with options: [lines] when a line count must drive a downstream integer parameter. For collections, first expose element identifiers with collection_element_identifiers, then count those identifier rows.

The reusable operation is still “produce a scalar file, then parameterize it”:

dataset -> wc_gnu(options: [lines]) -> param_value_from_file(param_type: integer)

For collection non-empty booleans, the corpus adds a tabular boolean step:

collection -> collection_element_identifiers -> wc_gnu -> column_maker(c1 != 0) -> param_value_from_file(param_type: boolean)

That final shape belongs operationally to conditional-gate-on-nonempty-result when it feeds when.

Tabular Scalar Round Trip

Some workflows compute one value in tabular-land, then escape back to parameter-land. Consensus peaks uses table_compute to get a minimum value, then reads that value back with param_value_from_file. MGnify uses column_maker only to turn a count into c1 != 0 before reading the result as a boolean.

Keep the tabular mechanics on the tabular page. This page owns the escape hatch from one-value dataset to typed parameter.

Idiomatic Shapes

Conceptual scalar read:

tool_id: param_value_from_file
in:
  - id: input1
    source: upstream_scalar_file
out:
  - id: integer_param
tool_state:
  input1:
    __class__: ConnectedValue
  param_type: integer
  remove_newlines: true

Conceptual count-to-integer:

dataset -> wc_gnu(options: [lines]) -> param_value_from_file(param_type: integer)

Conceptual collection non-empty boolean:

collection -> collection_element_identifiers -> wc_gnu -> column_maker(c1 != 0) -> param_value_from_file(param_type: boolean)

Pitfalls

  • Do not connect the dataset output when the downstream tool expects a typed parameter port.
  • Do not connect the wrong typed output port after changing param_type.
  • Do not leave newlines in one-value scalar files unless downstream text syntax requires them.
  • Do not treat wc_gnu output as numeric until param_value_from_file converts it.
  • Do not bury the operation under wc_gnu; counts are just one upstream scalar-producing recipe.
  • Do not duplicate conditional-gate-on-nonempty-result. If the user story is “skip when empty,” the conditional page owns the recommendation.
  • Do not present MGnify’s four-step boolean shim as best. It is corpus-backed but clunky and pending verified-pattern issue #84.

See Also

IWC exemplars4 anchors

IWC Exemplars

VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1high

Reads homozygous read coverage as a float and estimated genome size as an integer parameter.

epigenetics/consensus-peaks/consensus-peaks-atac-cutandrunhigh

Converts table-derived minima and replicate counts through text and integer parameter ports before downstream subsampling.

virology/influenza-isolates-consensus-and-subtyping/influenza-consensus-and-subtypinghigh

Turns line counts into integer parameters used as collection duplication counts.

amplicon/amplicon-mgnify/mgnify-amplicon-pipeline-v5-rrna-prediction/mgnify-amplicon-pipeline-v5-rrna-predictionhigh

Counts collection identifiers, converts the count to a boolean, then reads it through boolean_param.

Incoming References (5)

  • Parameter: compose runtime text parameterrelated pattern— Use compose_text_param to build connected text expressions from constants plus runtime scalar values.
  • Tabular: compute a new columnrelated pattern— Use column_maker (Add_a_column1) with strict error_handling to insert/replace a computed column. Per-expression-kind auto_col_types rule.
  • Iwc Conditionals Surveyrelated note— Corpus survey of Galaxy conditional step usage in IWC, covering when-gates, boolean shims, and routed output selection.
  • Iwc Parameter Derivation Surveyrelated note— Corpus survey of Galaxy workflow recipes that turn upstream data, metadata, or small files into runtime parameters.
  • Iwc Runtime Parameter Shims Surveyrelated pattern— Focused survey of tiny IWC runtime parameter shims for flags, enums, counts, booleans, and composed text.